Table 1.

The ranking of compounds from Glide docking and their calculated MM/GBSA binding energies (kcal/mol) using Prime of substituted pyrimidines and pteridinones in the ATP-binding site of the NTKD of RSK2. Inhibitory activity of compounds in the TR-FRET kinase assay against RSK2 (methods described in Casalvieri et al., 2020) given as the half-maximal inhibitory concentrations (IC₅₀) or percentage inhibition; values are the mean ± S.D. (n = 3).

Compound	Rank from Glide output	Dock Score	Calculated MM/GBSA binding energy (kcal/mol)	RSK2 Inhibition
BI-D1870 R-isomer	2	−10.6	−86.3	23.3 ± 8.2 nM
BI-D1870 S-isomer	7	−10.1	−79.9
BI-D1870 R-isomer deprotonated	40	−7.0	−61.8
BI-D1870 S-isomer deprotonated	43	−6.8	−57.5
BI-D1870 R-isomer protonated	55	−1.3	−31.5
BI-D1870 S-isomer protonated	54	−1.3	−27.3
24R-isomer	6	−10.1	−80.8	71% @ 10 μM
24S-isomer	16	−9.7	−83.0
25R-isomer	29	−8.0	−63.4	43% @ 10 μM
25S-isomer	35	−7.3	−67.1
26R-isomer	48	−5.7	−69.0	739 ± 14.1 nM
26S-isomer	30	−8.0	−67.9
27R-isomer	24	−8.6	−80.8	54.8 ± 1.4 nM
27S-isomer	28	−8.1	−76.5
28R-isomer	10	−10.0	−82.4	25.4 ± 3.2 nM
28S-isomer	17	−9.4	−74.6
28R-isomer protonated	57	−0.6	−31.7
28S-isomer protonated	58	−0.6	−25.2
29R-isomer	18	−9.3	−85.1	71.5 ± 10.3 nM
29S-isomer	22	−8.7	−78.1
30R-isomer	20	−8.8	−80.7	141 ± 25.7 nM
30S-isomer	23	−8.6	−80.9
31R-isomer	11	−9.9	−90.7	83% @ 10 μM
31S-isomer	31	−7.9	−78.1
31R-isomer deprotonated	39	−7.0	−69.4
31S-isomer deprotonated	32	−7.9	−66.1
31R-isomer protonated	50	−2.8	−56.5
31S-isomer protonated	51	−2.8	−45.1
32R-isomer	36	−7.2	−69.0	78% @ 10 μM
32S-isomer	25	−8.4	−78.2
32R-isomer deprotonated	37	−7.1	−74.5
32S-isomer deprotonated	27	−8.1	−71.8
32R-isomer protonated	49	−3.1	−60.6
32S-isomer protonated	52	−2.7	−47.5
33R-isomer	5	−10.3	−80.3	18.2 ± 1.4 nM
33S-isomer	4	−10.3	−81.1
33R-isomer deprotonated	26	−8.4	−60.5
33S-isomer deprotonated	42	−6.9	−53.6
33R-isomer protonated	53	−2.0	−25.1
33S-isomer protonated	41	−7.0	−48.1
34	1	−10.8	−81.3	17.6 ± 1.4 nM
34 deprotonated	21	−8.8	−69.9
35	12	−9.9	−77.1	38.3 ± 7.9 nM
35 deprotonated	34	−7.3	−50.5
36	3	−10.5	−81.8	23.4 ± 4.7 nM
37	15	−9.8	−76.9	24.7 ± 1.8 nM
38	14	−9.8	−54.0	45% @ 10 μM
38 deprotonated	44	−6.6	−28.9
39R-isomer	8	−10.0	−66.5	83% @ 10 μM
39S-isomer	9	−10.0	−66.7
39R-isomer deprotonated	33	−7.6	−58.5
39S-isomer deprotonated	38	−7.1	−58.7
43	13	−9.8	−58.9	72% @ 10 μM
43 deprotonated	46	−6.2	−34.5
44	19	−9.0	−53.2	38% @ 10 μM
44 deprotonated	45	−6.2	−29.4
44 protonated	47	−5.9	−21.7
44 deprotonated/protonated	56	−0.7	−0.1